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<span class="Apple-style-span" style="font-family: Tahoma, Verdana, Arial, sans-serif; font-size: 13.3333px; color: rgb(68, 68, 68); ">Dear Users<div><br></div><div><div>I want to calculate the diffusion constant of one molecule in water.</div><div>I make this calculation in the followin way:</div><div><br></div><div>Obtaining a continuos trajectory</div><div><br></div><div>1) trjconv -f traj.trr -pbc nojump -o traj_nojump.xtc</div><div><br></div><div><br></div><div>Obtaining the msd of the solute, <span class="ecxApple-style-span" style="font-size: 13.3333px; ">removing the center of mass of the system</span></div><div><br></div><div>Firt way:</div><div><br></div><div>2a) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -o msd_solute.xvg -rmcomm</div><div><br></div><div>I choose SOLUTE</div><div><br></div><div><br></div><div>Second way</div><div><br></div><div><br></div><div>2b) g_msd -f traj_nojump.xtc -s topol.tpr -n index.ndx -rmcomm -o msd_solute.xvg -rmcomm -mv</div><div> </div><div><br></div><div>I choose SOLUTE</div><div><br></div><div><br></div><div>There are significative differences in the results?</div><div><br></div><div>according to the gromacs manual -mv option is used in molecules,</div><div><br></div><div><br></div><div>What is the correct step, 2a or 2b?</div><div><br></div><div><br></div><div><br></div><div>Regards</div><div><br></div><div>Teobaldo</div></div><div><br></div></span><br><div>___________________________________________________________</div><div>Teobaldo Ricardo Cuya Guizado, Msc.</div><div>Physics Department</div><div>Pontificia Universidade Catolica de Rio de Janeiro</div><div><div>Rua Marquês de São Vicente, 225</div><div>22451-900 Gávea - Rio de Janeiro - RJ BRASIL</div><div>Phone: 55-21-7613-3843</div><div>e-mail: trcuyag@gmail.com</div><div>Web page: http://www.trcuyag.blogspot.com</div></div><div>___________________________________________________________</div><br><br> <br /><hr />Découvrez comment échanger avec vos vrais amis. <a href='http://go.microsoft.com/?linkid=9734392' target='_new'>Découvrez comment!</a></body>
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